title: The control region of mitochondrial DNA shows an unusual CpG and non-CpG methylation pattern.
abstract: DNA methylation is a common epigenetic modification of the mammalian genome. Conflicting data regarding the possible presence of methylated cytosines within mitochondrial DNA (mtDNA) have been reported. To clarify this point, we analysed the methylation status of mtDNA control region (D-loop) on human and murine DNA samples from blood and cultured cells by bisulphite sequencing and methylated/hydroxymethylated DNA immunoprecipitation assays. We found methylated and hydroxymethylated cytosines in the L-strand of all samples analysed. MtDNA methylation particularly occurs within non-C-phosphate-G (non-CpG) nucleotides, mainly in the promoter region of the heavy strand and in conserved sequence blocks, suggesting its involvement in regulating mtDNA replication and/or transcription. We observed DNA methyltransferases within the mitochondria, but the inactivation of Dnmt1, Dnmt3a, and Dnmt3b in mouse embryonic stem (ES) cells results in a reduction of the CpG methylation, while the non-CpG methylation shows to be not affected. This suggests that D-loop epigenetic modification is only partially established by these enzymes. Our data show that DNA methylation occurs in the mtDNA control region of mammals, not only at symmetrical CpG dinucleotides, typical of nuclear genome, but in a peculiar non-CpG pattern previously reported for plants and fungi. The molecular mechanisms responsible for this pattern remain an open question.
authors.affiliation: 1Department of Cell Biology, University of Calabria, Rende 87036, Italy.
authors.forename: Dina
authors.initials: D
authors.lastname: Bellizzi
authors.forename: Patrizia
authors.initials: P
authors.lastname: D'Aquila
authors.forename: Teresa
authors.initials: T
authors.lastname: Scafone
authors.forename: Marco
authors.initials: M
authors.lastname: Giordano
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Riso
authors.forename: Andrea
authors.initials: A
authors.lastname: Riccio
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Passarino
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000818:Animals; D002460:Cell Line; D018899:CpG Islands; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000378:metabolism; D019175:DNA Methylation; D004272:DNA, Mitochondrial / Q000097:blood / Q000235:genetics*; D049308:Dioxygenases / Q000378:metabolism; D005260:Female; D006801:Humans; D019901:Locus Control Region; D008297:Male; D051379:Mice; D008875:Middle Aged; D008928:Mitochondria / Q000235:genetics / Q000378:metabolism; D000097584:DNA Methyltransferase 3B
chemical_list: D004248:DNA (Cytosine-5-)-Methyltransferases; D004272:DNA, Mitochondrial; D049308:Dioxygenases; D000097584:DNA Methyltransferase 3B; C578792:TET3 protein, human
keywords: 5-hydromethylcytosine; 5-methylcytosine; CpG methylation; mitochondrial D-loop region; non-CpG methylation